def test_n_cores(self):
with make_case(np.uint16, (10, 20, 30),
return_path=True) as (glob_expr, dest, volume):
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "tiff", "--n-cores", "1"
])
def test_zarr(self):
with make_case(np.uint16, (128, 128, 128),
return_path=True) as (glob_expr, dest, volume):
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "zarr"
])
store = zarr.NestedDirectoryStore(os.path.join(dest, "1_1_1"))
z_arr = zarr.open(store, "r")
self.assertSequenceEqual(z_arr.shape, (128, 128, 128))
def test_tiff(self):
with make_case(np.uint16, (256, 256, 256),
return_path=True) as (glob_expr, dest, volume):
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "tiff"
])
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "tiff", "--chunk-size", "128,128,128"
])
def test_write_chunk_128(self):
with make_case(np.uint16, (200, 200, 200), return_path=True) \
as (glob_expr, dest, stack):
bfs = BlockfsStack(glob_expr, dest, chunk_size=(128, 128, 128))
bfs.write_level_1(silent=True, n_cores=1)
directory_filename = \
os.path.join(dest, "1_1_1", BlockfsStack.DIRECTORY_FILENAME)
directory = Directory.open(directory_filename)
np.testing.assert_array_equal(stack[:128, :128, :128],
directory.read_block(0, 0, 0))
np.testing.assert_array_equal(stack[128:, 128:, 128:],
directory.read_block(128, 128, 128))
def test_write_oddly_shaped(self):
with make_case(np.uint16, (100, 100, 100), return_path=True)\
as (glob_expr, dest, stack):
bfs = BlockfsStack(glob_expr, dest)
bfs.write_level_1(silent=True, n_cores=1)
directory_filename =\
os.path.join(dest, "1_1_1", BlockfsStack.DIRECTORY_FILENAME)
directory = Directory.open(directory_filename)
np.testing.assert_array_equal(stack[:64, :64, :64],
directory.read_block(0, 0, 0))
np.testing.assert_array_equal(stack[64:, 64:, 64:],
directory.read_block(64, 64, 64))
def test_write_level_1(self):
with make_case(np.uint16, (100, 200, 300)) as (stack, npstack):
stack.write_level_1()
block_0_64_256 = tifffile.imread(
os.path.join(stack.dest, "1_1_1", "256-300_64-128_0-64.tiff"))
np.testing.assert_equal(block_0_64_256, npstack[:64, 64:128, 256:])
for (x0, x1), (y0, y1), (z0, z1) in itertools.product(
zip(stack.x0(1), stack.x1(1)), zip(stack.y0(1),
stack.y1(1)),
zip(stack.z0(1), stack.z1(1))):
path = stack.fname(1, x0, x1, y0, y1, z0, z1)
block = tifffile.imread(path)
np.testing.assert_equal(block, npstack[z0:z1, y0:y1, x0:x1])
def test_write_level_2(self):
with make_case(np.uint16, (100, 201, 300)) as (stack, npstack):
stack.write_level_1()
stack.write_level_n(2)
block = tifffile.imread(
os.path.join(stack.dest, "2_2_2", "128-150_64-101_0-50.tiff"))
self.assertSequenceEqual(block.shape, (50, 101 - 64, 150 - 128))
s32 = npstack.astype(np.uint32)
first = (s32[0, 128, 256] + s32[1, 128, 256] + s32[0, 129, 256] +
s32[1, 129, 256] + s32[0, 128, 257] + s32[1, 128, 257] +
s32[0, 129, 257] + s32[1, 129, 257]) // 8
self.assertEqual(block[0, 0, 0], first)
last = (s32[-2, -1, -2] + s32[-1, -1, -2] + s32[-2, -1, -1] +
s32[-1, -1, -1]) // 4
self.assertEqual(block[-1, -1, -1], last)
def test_write_level_1(self):
with make_case(np.uint16, (100, 200, 300), klass=NGFFStack) \
as (stack, npstack):
stack.create()
stack.write_info_file(1)
stack.write_level_1()
z_arr = stack.zgroup["0"]
block_0_64_256 = z_arr[0, 0, :64, 64:128, 256:]
np.testing.assert_equal(block_0_64_256, npstack[:64, 64:128, 256:])
for (x0, x1), (y0, y1), (z0, z1) in itertools.product(
zip(stack.x0(1), stack.x1(1)), zip(stack.y0(1),
stack.y1(1)),
zip(stack.z0(1), stack.z1(1))):
block = z_arr[0, 0, z0:z1, y0:y1, x0:x1]
np.testing.assert_equal(block, npstack[z0:z1, y0:y1, x0:x1])
def test_write_level_1(self):
with make_case(np.uint16, (100, 200, 300), klass=ZarrStack) \
as (stack, npstack):
stack.write_level_1()
dest_lvl1 = os.path.join(stack.dest, "1_1_1")
store = zarr.NestedDirectoryStore(dest_lvl1)
z_arr = zarr.open(store, mode='r')
block_0_64_256 = z_arr[:64, 64:128, 256:]
np.testing.assert_equal(block_0_64_256, npstack[:64, 64:128, 256:])
for (x0, x1), (y0, y1), (z0, z1) in itertools.product(
zip(stack.x0(1), stack.x1(1)), zip(stack.y0(1),
stack.y1(1)),
zip(stack.z0(1), stack.z1(1))):
block = z_arr[z0:z1, y0:y1, x0:x1]
np.testing.assert_equal(block, npstack[z0:z1, y0:y1, x0:x1])
def test_write_info_file(self):
with make_case(np.uint16, (101, 200, 300)) as (stack, npstack):
stack.write_info_file(2)
with open(os.path.join(stack.dest, "info")) as fd:
info = json.load(fd)
self.assertEqual(info["data_type"], "uint16")
self.assertEqual(info["num_channels"], 1)
scales = info["scales"]
self.assertEqual(len(scales), 2)
self.assertSequenceEqual(scales[0]["chunk_sizes"][0], (64, 64, 64))
self.assertEqual(scales[0]["encoding"], "raw")
self.assertEqual(scales[0]["key"], "1_1_1")
self.assertSequenceEqual(scales[0]["resolution"],
(1800, 1800, 2000))
self.assertSequenceEqual(scales[0]["size"], (300, 200, 101))
self.assertSequenceEqual(scales[0]["voxel_offset"], (0, 0, 0))
self.assertSequenceEqual(scales[1]["size"], (150, 100, 51))
def test_coordinates(self):
with make_case(np.uint16, (100, 200, 300)) as (stack, npstack):
self.assertEqual(stack.n_x(1), 300 // 64 + 1)
self.assertEqual(stack.n_x(2), 3)
self.assertEqual(stack.n_x(3), 2)
self.assertEqual(stack.n_x(4), 1)
self.assertEqual(stack.n_x(5), 1)
self.assertEqual(stack.n_y(1), 4)
self.assertEqual(stack.n_y(2), 2)
self.assertEqual(stack.n_z(1), 2)
self.assertEqual(stack.n_z(2), 1)
self.assertSequenceEqual(stack.z0(1).tolist(), (0, 64))
self.assertSequenceEqual(stack.z1(1).tolist(), (64, 100))
self.assertSequenceEqual(stack.y0(1).tolist(), (0, 64, 128, 192))
self.assertSequenceEqual(stack.y1(1).tolist(), (64, 128, 192, 200))
self.assertSequenceEqual(stack.x0(2).tolist(), (0, 64, 128))
self.assertSequenceEqual(stack.x1(2).tolist(), (64, 128, 150))
def test_write_level_2(self):
with make_case(np.uint16, (100, 201, 300), klass=ZarrStack) \
as (stack, npstack):
stack.write_level_1()
stack.write_level_n(2)
dest_lvl2 = os.path.join(stack.dest, "2_2_2")
store = zarr.NestedDirectoryStore(dest_lvl2)
z_arr = zarr.open(store, "r")
block = z_arr[0:50, 64:101, 128:150]
self.assertSequenceEqual(block.shape, (50, 101 - 64, 150 - 128))
s32 = npstack.astype(np.uint32)
first = (s32[0, 128, 256] + s32[1, 128, 256] + s32[0, 129, 256] +
s32[1, 129, 256] + s32[0, 128, 257] + s32[1, 128, 257] +
s32[0, 129, 257] + s32[1, 129, 257]) // 8
self.assertEqual(block[0, 0, 0], first)
last = (s32[-2, -1, -2] + s32[-1, -1, -2] + s32[-2, -1, -1] +
s32[-1, -1, -1]) // 4
self.assertEqual(block[-1, -1, -1], last)
def test_blockfs(self):
with make_case(np.uint16, (256, 256, 256), return_path=True) as \
(glob_expr, dest, volume):
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "blockfs"
])
directory = Directory.open(
os.path.join(dest, "1_1_1", BlockfsStack.DIRECTORY_FILENAME))
block = directory.read_block(0, 0, 0)
np.testing.assert_array_equal(block, volume[:64, :64, :64])
main([
"--source", glob_expr, "--dest", dest, "--levels", "2",
"--format", "blockfs", "--chunk-size", "128,128,128"
])
directory = Directory.open(
os.path.join(dest, "1_1_1", BlockfsStack.DIRECTORY_FILENAME))
block = directory.read_block(0, 0, 0)
np.testing.assert_array_equal(block, volume[:128, :128, :128])
def test_write_info_file(self):
with make_case(np.uint16, (101, 200, 300), klass=NGFFStack) \
as (stack, npstack):
stack.create()
stack.write_info_file(2)
scale_md = stack.zgroup.attrs["multiscales"][0]
for i, dataset_md in enumerate(scale_md["datasets"]):
self.assertEqual(str(i), dataset_md["path"])
with open(os.path.join(stack.dest, "info")) as fd:
info = json.load(fd)
self.assertEqual(info["data_type"], "uint16")
self.assertEqual(info["num_channels"], 1)
scales = info["scales"]
self.assertEqual(len(scales), 2)
self.assertSequenceEqual(scales[0]["chunk_sizes"][0], (64, 64, 64))
self.assertEqual(scales[0]["encoding"], "raw")
self.assertEqual(scales[0]["key"], "1_1_1")
self.assertSequenceEqual(scales[0]["resolution"],
(1800, 1800, 2000))
self.assertSequenceEqual(scales[0]["size"], (300, 200, 101))
self.assertSequenceEqual(scales[0]["voxel_offset"], (0, 0, 0))
self.assertSequenceEqual(scales[1]["size"], (150, 100, 51))
def test_init(self):
with make_case(np.uint16, (100, 200, 300)) as (stack, npstack):
self.assertEqual(stack.x_extent, 300)
self.assertEqual(stack.y_extent, 200)
self.assertEqual(stack.z_extent, 100)
